Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_104913141.1 C3B54_RS02765 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_002950575.1:WP_104913141.1 Length = 507 Score = 348 bits (893), Expect = e-100 Identities = 194/481 (40%), Positives = 279/481 (58%), Gaps = 14/481 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 H+I G++ + G F++I+P + +A G A +ID A+ AA A W K + E Sbjct: 22 HWIGGQWTKPVKGNYFEDISPVNGKPFCEIARGTAEDIDAALDAAHAAAPA-WGKASTTE 80 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R AVL K+ D+I E L+V E+ D GKP + + DIP AA +F +F +R + Sbjct: 81 RAAVLNKIADVIDANVEMLAVAETWDNGKPIRETLNADIPLAADHFRYFVAAVRAQDGDF 140 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +MD Y P+GV+G I PWN P+L+ WKLAPAL+AGN VV+KPAE TP + V Sbjct: 141 QEMDGDTTAYHYHEPLGVVGQIIPWNFPILMAAWKLAPALSAGNAVVLKPAEQTPASILV 200 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 LAE+ D +P GV+N+V+GFG AG L P + I+FTGETTTG++I+ A+ + Sbjct: 201 LAELIGDI-LPPGVLNIVNGFGA-EAGKPLASSPRIRKIAFTGETTTGRLILQYASANII 258 Query: 253 RLSYELGGKNPNVIFADSN------LDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306 + ELGGK+PN+ F D + D+ E + +F NQGEVC C SR +++ Y++ Sbjct: 259 PTTLELGGKSPNIFFDDVSQEKDDFYDKAQEGFVLFAF-NQGEVCTCPSRALIQKSHYDS 317 Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE-- 364 FL V +TK+ + G+P D T+VGA S++ E++ YI + +EG T++ GG R + Sbjct: 318 FLGDAVERTKKAIQGNPLDTDTQVGAQASNDQLEKILSYIDIGKQEGATLVCGGDRVDLG 377 Query: 365 -GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 L GY++EP I G R+ +EEIFGPVV V FD ++ ++ NDT YGL A VW Sbjct: 378 GDLADGYYVEPAIFEG-NNKMRLFQEEIFGPVVAVTSFDDYDDAIQIANDTLYGLGAGVW 436 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483 + + A+R I+AG VWVN + FGG K SGIGRE + Y + N+ Sbjct: 437 SRNGNTAYRAGRDIQAGRVWVNNYHAYPAGAAFGGYKSSGIGRENNKLALSHYQQTKNLL 496 Query: 484 I 484 + Sbjct: 497 V 497 Lambda K H 0.318 0.136 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 651 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 507 Length adjustment: 34 Effective length of query: 452 Effective length of database: 473 Effective search space: 213796 Effective search space used: 213796 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory